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- PDB-6aci: Crystal structure of EPEC effector NleB in complex with FADD deat... -

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Basic information

Entry
Database: PDB / ID: 6aci
TitleCrystal structure of EPEC effector NleB in complex with FADD death domain
Components
  • FAS-associated death domain protein
  • T3SS secreted effector NleB homolog
KeywordsTOXIN / glycosyltransferase
Function / homology
Function and homology information


protein-arginine N-acetylglucosaminyltransferase activity / symbiont-mediated suppression of host programmed cell death / Transferases; Glycosyltransferases; Hexosyltransferases / manganese ion binding / toxin activity / symbiont-mediated suppression of host NF-kappaB cascade / cytosolic large ribosomal subunit / host cell cytoplasm / structural constituent of ribosome / translation / extracellular region
Similarity search - Function
SseK/NleB family / Death Domain, Fas / Death Domain, Fas / Death domain / : / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily ...SseK/NleB family / Death Domain, Fas / Death Domain, Fas / Death domain / : / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Protein-arginine N-acetylglucosaminyltransferase NleB1 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsDing, J. / Shao, F.
CitationJournal: Mol.Cell / Year: 2019
Title: Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector.
Authors: Ding, J. / Pan, X. / Du, L. / Yao, Q. / Xue, J. / Yao, H. / Wang, D.C. / Li, S. / Shao, F.
History
DepositionJul 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T3SS secreted effector NleB homolog
H: FAS-associated death domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1794
Polymers45,7192
Non-polymers4592
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-17 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.590, 84.590, 145.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-768-

HOH

31A-829-

HOH

41A-857-

HOH

51A-858-

HOH

61H-219-

HOH

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Components

#1: Protein T3SS secreted effector NleB homolog


Mass: 35105.441 Da / Num. of mol.: 1 / Mutation: K115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Strain: E2348/69 / EPEC / Gene: E2348C_3231 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7UI21
#2: Protein FAS-associated death domain protein / FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of ...FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of receptor induced toxicity / Protein FADD


Mass: 10614.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Plasmid: pGEX6p / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13158
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.5 M Sodium chloride, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.87→36.63 Å / Num. obs: 50430 / % possible obs: 99.6 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.3
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 7314 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+66 / Resolution: 1.87→36.589 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.77
RfactorNum. reflection% reflection
Rfree0.2094 2563 5.09 %
Rwork0.1644 --
obs0.1666 50377 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→36.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 26 436 3630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173261
X-RAY DIFFRACTIONf_angle_d1.6034415
X-RAY DIFFRACTIONf_dihedral_angle_d14.1251225
X-RAY DIFFRACTIONf_chiral_restr0.085477
X-RAY DIFFRACTIONf_plane_restr0.009573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9060.26281470.21252609X-RAY DIFFRACTION100
1.906-1.94490.21851510.1952635X-RAY DIFFRACTION100
1.9449-1.98720.21111510.18552617X-RAY DIFFRACTION100
1.9872-2.03340.2361460.17522637X-RAY DIFFRACTION100
2.0334-2.08420.24151250.17972629X-RAY DIFFRACTION100
2.0842-2.14060.19521470.16242647X-RAY DIFFRACTION100
2.1406-2.20360.20681420.16092633X-RAY DIFFRACTION100
2.2036-2.27470.21361460.16562651X-RAY DIFFRACTION100
2.2747-2.3560.23841690.16822638X-RAY DIFFRACTION100
2.356-2.45030.19081420.16462630X-RAY DIFFRACTION100
2.4503-2.56180.20731290.17472686X-RAY DIFFRACTION100
2.5618-2.69680.22481310.18572655X-RAY DIFFRACTION100
2.6968-2.86570.26561510.1882672X-RAY DIFFRACTION100
2.8657-3.08680.22221390.17262660X-RAY DIFFRACTION100
3.0868-3.39730.20471330.16282719X-RAY DIFFRACTION100
3.3973-3.88840.16951620.14152672X-RAY DIFFRACTION100
3.8884-4.89710.18731430.12992739X-RAY DIFFRACTION100
4.8971-36.59570.21861090.17862685X-RAY DIFFRACTION93

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